This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Protein structures can be determined through either experimental methods, such as X-ray crystallography and Nuclear Magnetic Resonance (NMR) technology, or theoretical methods, such as protein folding and homology modeling. However, many of determine protein structures are usually not as accurate as desired. Therefore, their applications have been severely limited in important fields, and structure refinement is always important and critical. In recent decades, the number of high resolution protein structures determined and deposited in PDB database is increasing, which makes it possible to conduct statistical analysis in the structural database. In this project, we propose a knowledge-based approach for protein structure refinement.